Parse file to remove two characters from the ends of a lot of lines
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0
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4.8 years ago

Dear all,

I have a txt file with data of this form:

@HWI-ST999:188:C49E6ACXX:8:1101:11404:1998/1
NCGAGGGATGGGAGACCTGGTTGGAAATCCGTGGCTGTTTGGTTGGGGGAT
+
#4=DDFFDHDHHGJIIJIJIFHIIIJJIJJJDHIGIEDGHGI=CGHJJH9>
@HWI-ST999:188:C49E6ACXX:8:1101:1754:2212/1
TCGAATGCATGATAACAATAACCCTGGAACAGGCAACCGTTGTCCCTGACC
+
CCCFFFFFHHHGHJJJJJJJJJJJJJJJJJJJJIJJJJJIIJJJJJJJJJJ

I would like to remove the /1 of the end of every 5th line. Is this possible with a one liner in bash, maybe with sed (OSX)?

Context: I extracted reads from a bam file with Bam2Fastq into the format fastq. But the subsequent processing does not cope with the /1 or /2 in my two files of paired-end reads.

command line OSX • 1.5k views
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Would be more accurate to call this a fastq file, it's not just a txt file...

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But someone who does not know what a fastq format is would be put off by it. And basically it can be called a txt file.

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That doesn't make sense. You don't want answers from people who don't know what a fastq file is. This is biostars. We read fastq files at breakfast like normal people read the newspaper.

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For this question it is unnecessary to know anything about biology. And I want to keep the question as easy to understand as possible. It would be more accurate to call it a fastq file, I guess, but not helpful here and in some cases maybe distracting. Although I guess 99.9% of people here know that it is a fastq file. And for those, I don't need to make it clear anyways.

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4.8 years ago
george.ry ★ 1.1k

New file: sed '1~4s/\/1$//' myfile.fq > mynewfile.fq

Inplace: sed -i '1~4s/\/1$//' myfile.fq

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returns: sed: 1: "1~4s/\/1$//": invalid command code ~

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Am I right in guessing that you're on a Mac, then?

// EDIT // Answering myself, the answer is that you are. OSX doesn't have GNU sed, so you'll need to install it with homebrew (etc).

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$ brew list
boost       hdf5        libxml2     sratoolkit  tophat
bowtie2     htslib      openssl     szip        wget
gnu-sed     libmagic    samtools    tbb

I installed gnu-sed with homebrew. Now it returns: sed: 1: "s_188_1_seq.txt": bad flag in substitute command: 's'

EDIT: homebrew put it in a weird location, so I used it like this now:

/usr/local/Cellar/gnu-sed/4.2.2/bin/gsed -i '1~4s/\/1$//' s_188_1_seq.txt

And it worked! Thank you. <3

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